static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
gmx::DefaultRandomEngine * rng, rvec max_rot)
{
mat4 mt1, mt2, mr[DIM], mtemp1, mtemp2, mtemp3, mxtot, mvtot;
rvec xcm;
real phi;
int i, m;
gmx::UniformRealDistribution<real> dist(-1.0, 1.0);
clear_rvec(xcm);
for (i = 0; (i < natoms); i++)
{
for (m = 0; (m < DIM); m++)
{
xcm[m] += x[i][m]/natoms; /* get center of mass of one molecule */
}
}
fprintf(stderr, "center of geometry: %f, %f, %f\n", xcm[0], xcm[1], xcm[2]);
/* move c.o.ma to origin */
gmx_mat4_init_translation(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1);
for (m = 0; (m < DIM); m++)
{
phi = M_PI*max_rot[m]*dist(*rng)/180;
gmx_mat4_init_rotation(m, phi, mr[m]);
}
gmx_mat4_init_translation(xcm[XX], xcm[YY], xcm[ZZ], mt2);
/* For gmx_mat4_mmul() we need to multiply in the opposite order
* compared to normal mathematical notation.
*/
gmx_mat4_mmul(mtemp1, mt1, mr[XX]);
gmx_mat4_mmul(mtemp2, mr[YY], mr[ZZ]);
gmx_mat4_mmul(mtemp3, mtemp1, mtemp2);
gmx_mat4_mmul(mxtot, mtemp3, mt2);
gmx_mat4_mmul(mvtot, mr[XX], mtemp2);
for (i = 0; (i < natoms); i++)
{
gmx_mat4_transform_point(mxtot, x[i], xrot[i]);
gmx_mat4_transform_point(mvtot, v[i], vrot[i]);
}
}
static void rot_conf(t_atoms *atoms, rvec x[], rvec v[], real trans, real angle,
rvec head, rvec tail, int isize, atom_id index[],
rvec xout[], rvec vout[])
{
rvec arrow, xcm;
real theta, phi, arrow_len;
mat4 Rx, Ry, Rz, Rinvy, Rinvz, Mtot;
mat4 temp1, temp2, temp3;
vec4 xv;
int i, ai;
rvec_sub(tail, head, arrow);
arrow_len = norm(arrow);
if (debug)
{
fprintf(debug, "Arrow vector: %10.4f %10.4f %10.4f\n",
arrow[XX], arrow[YY], arrow[ZZ]);
fprintf(debug, "Effective translation %g nm\n", trans);
}
if (arrow_len == 0.0)
{
gmx_fatal(FARGS, "Arrow vector not given");
}
/* Copy all aoms to output */
for (i = 0; (i < atoms->nr); i++)
{
copy_rvec(x[i], xout[i]);
copy_rvec(v[i], vout[i]);
}
/* Compute center of mass and move atoms there */
clear_rvec(xcm);
for (i = 0; (i < isize); i++)
{
rvec_inc(xcm, x[index[i]]);
}
for (i = 0; (i < DIM); i++)
{
xcm[i] /= isize;
}
if (debug)
{
fprintf(debug, "Center of mass: %10.4f %10.4f %10.4f\n",
xcm[XX], xcm[YY], xcm[ZZ]);
}
for (i = 0; (i < isize); i++)
{
rvec_sub(x[index[i]], xcm, xout[index[i]]);
}
/* Compute theta and phi that describe the arrow */
theta = std::acos(arrow[ZZ]/arrow_len);
phi = std::atan2(arrow[YY]/arrow_len, arrow[XX]/arrow_len);
if (debug)
{
fprintf(debug, "Phi = %.1f, Theta = %.1f\n", RAD2DEG*phi, RAD2DEG*theta);
}
/* Now the total rotation matrix: */
/* Rotate a couple of times */
gmx_mat4_init_rotation(ZZ, -phi, Rz);
gmx_mat4_init_rotation(YY, M_PI/2-theta, Ry);
gmx_mat4_init_rotation(XX, angle*DEG2RAD, Rx);
Rx[WW][XX] = trans;
gmx_mat4_init_rotation(YY, theta-M_PI/2, Rinvy);
gmx_mat4_init_rotation(ZZ, phi, Rinvz);
gmx_mat4_mmul(temp1, Ry, Rz);
gmx_mat4_mmul(temp2, Rinvy, Rx);
gmx_mat4_mmul(temp3, temp2, temp1);
gmx_mat4_mmul(Mtot, Rinvz, temp3);
if (debug)
{
gmx_mat4_print(debug, "Rz", Rz);
gmx_mat4_print(debug, "Ry", Ry);
gmx_mat4_print(debug, "Rx", Rx);
gmx_mat4_print(debug, "Rinvy", Rinvy);
gmx_mat4_print(debug, "Rinvz", Rinvz);
gmx_mat4_print(debug, "Mtot", Mtot);
}
for (i = 0; (i < isize); i++)
{
ai = index[i];
gmx_mat4_transform_point(Mtot, xout[ai], xv);
rvec_add(xv, xcm, xout[ai]);
gmx_mat4_transform_point(Mtot, v[ai], xv);
copy_rvec(xv, vout[ai]);
}
}